ConvexML: Fast and accurate branch length estimation under irreversible mutation models, illustrated through applications to CRISPR/Cas9-based lineage tracing.

Sebastian Prillo, Akshay Ravoor, Nir Yosef, Yun S Song

Abstract readPreprint

In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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1 · What the graph read from it

What it found

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2 · The registry

The trial behind it

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3 · Its place in the literature

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0 citing papers in PubMed.

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4 · The record

Corrections and comments

Updated by
ConvexML: Fast and Accurate Branch Length Estimation under Irreversible Mutation Models, Illustrated through Applications to CRISPR/Cas9-Based Lineage Tracing.2026

5 · Who and what money

Authors and funding

4 authors.

Sebastian PrilloComputer Science Division, University of California, Berkeley, USA.

Akshay RavoorComputer Science Division, University of California, Berkeley, USA.

Nir YosefComputer Science Division, University of California, Berkeley, USA.

Yun S SongComputer Science Division, University of California, Berkeley, USA.ORCID 0000-0002-0734-9868

Funding

Scalable Computational Methods for Genealogical Inference: from species level to single cellsR01HG013117 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI Ian H Holmes, RASMUS NIELSEN · 2024 to 2026

$1.7M

Scalable Computational Methods for Genealogical Inference: from species level to single cellsR56HG013117 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI HOLMES, IAN H, NIELSEN, RASMUS · 2023 to 2023

$315k

NHGRI NIH HHS R01 HG013117NHGRI NIH HHS R56 HG013117

6 · The paper itself

Abstract

Branch length estimation is a fundamental problem in Statistical Phylogenetics and a core component of tree reconstruction algorithms. Traditionally, general time-reversible mutation models are employed, and many software tools exist for this scenario. With the advent of CRISPR/Cas9 lineage tracing technologies, there has been significant interest in the study of branch length estimation under

Indexed as

branch length estimationconvex optimizationCRISPR/Cas9irreversible mutation modelsMaximum likelihood estimationparsimonypseudocountssingle-cell lineage tracing

Identifiers

PMID38076815

DOI10.1101/2023.12.03.569785

PMCPMC10705529

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LicenceCC BY-NC-ND

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.